Crystal structure of AetD in complex with 5-bromo-L-tryptophan and two Fe2+

Experimental Data Snapshot

  • Resolution: 2.01 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

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The structural and functional investigation into an unusual nitrile synthase.

Li, H.Huang, J.W.Dai, L.Zheng, H.Dai, S.Zhang, Q.Yao, L.Yang, Y.Yang, Y.Min, J.Guo, R.T.Chen, C.C.

(2023) Nat Commun 14: 7425-7425

  • DOI: https://doi.org/10.1038/s41467-023-43285-0
  • Primary Citation of Related Structures:  
    8JI2, 8JI3, 8JI4, 8JI5, 8JI6, 8JI7

  • PubMed Abstract: 

    The biosynthesis of neurotoxin aetokthonotoxin (AETX) that features a unique structure of pentabrominated biindole nitrile involves a first-of-its-kind nitrile synthase termed AetD, an enzyme that shares very low sequence identity to known structures and catalyzes an unprecedented mechanism. In this study, we resolve the crystal structure of AetD in complex with the substrate 5,7-di-Br-L-Trp. AetD adopts the heme oxygenase like fold and forms a hydrophobic cavity within a helical bundle to accommodate the indole moiety. A diiron cluster comprising two irons that serves as a catalytic center binds to the carboxyl O and the amino N of the substrate. Notably, we demonstrate that the AetD-catalyzed reaction is independent of the bromination of the substrate and also solved crystal structures of AetD in complex with 5-Br-L-Trp and L-Trp. Altogether, the present study reveals the substrate-binding pattern and validates the diiron cluster-comprising active center of AetD, which should provide important basis to support the mechanistic investigations into this class of nitrile synthase.

  • Organizational Affiliation

    State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
249Aetokthonos hydrillicola Thurmond2011Mutation(s): 0 
Gene Names: aetD
Find proteins for A0A861B387 (Aetokthonos hydrillicola Thurmond2011)
Explore A0A861B387 
Go to UniProtKB:  A0A861B387
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A861B387
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.01 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.633α = 90
b = 65.633β = 90
c = 117.313γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Database references